Complex carbohydrates are integral, functioning components of essentially all living systems, playing critical roles in an enormous variety of biological processes and recognition events. Yet, their detailed structural determination remains difficult. While mass spectrometry can provide important information about carbohydrate structures, a determination of the stereochemistry of individual monosaccharide ions that arise by fragmentation of larger carbohydrate structures is not generally possible. Also, analysis of mixtures of isomeric oligosaccharides by mass spectrometry remains difficult because the fundamental charge/mass ratio alone does not physically resolve isomeric structures. Thus, the goal of this project is to develop an analytical instrument that will markedly improve capabilities in the structural determination of complex carbohydrates by enabling isomeric structures to be resolved. The proposed instrument will be based on the principles of both ion trap mass spectrometry and ion mobility spectrometry. In its final form, the instrument will have an electrospray ionization (ESI) source coupled to a double gate ion mobility spectrometer (IMS). The double gate IMS, separating ions on the basis of size and shape rather than mass, will serve to select specific oligosaccharide isomers for injection into an ion trap mass spectrometer (ITMS). Pulses of the mobility-selected oligosaccharide will be concentrated in the ITMS followed by collision induced dissociation to generate ions of selected sugar monomers. These monomers will then be injected into a second, tandem IMS to identify the stereochemistry and anomeric configuration of monomer ions. By the separation and introduction of single oligosaccharides into the ITMS with dissociation and identification of the monomeric sugars, complete structural analysis of complex oligosaccharides may be possible. The critical steps in this plan are the production of monosaccharides by fragmentation in the ion trap and the separation of monosaccharides by IMS. Thus, the R21 phase of the project proposes to develop novel MS methods for the fragmentation of oligosaccharides and novel IMS methods for the separation of oligosaccharides as well as stereoisomeric and anomeric pairs of monosaccharide ions. In the R33 phase an IMS-IT-IMS instrument will be constructed, characterized and demonstrated for the elucidation of oligosaccharide structures. The overall instrument proposed in this grant application has the potential to generate data never before possible on this important and enigmatic class of biological compounds and will provide a novel tool for the emerging field of Structural Glycomics. To date, the detailed chemical structures of most naturally occurring oligosaccharides have eluded identification solely by mass spectrometry. Successful completion of this project will provide a tool which will not only extend the analytical power of mass spectrometry to analysis of isomeric mono- and oligosaccharides, but will also be generally useful for analysis of all types of molecules where ambiguity may exist concerning possible isomeric variants in mixtures or isomeric monomeric constituents of larger polymeric molecules.